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2.
Philos Trans A Math Phys Eng Sci ; 380(2233): 20210307, 2022 Oct 03.
Article in English | MEDLINE | ID: covidwho-1992464

ABSTRACT

Transmission models for infectious diseases are typically formulated in terms of dynamics between individuals or groups with processes such as disease progression or recovery for each individual captured phenomenologically, without reference to underlying biological processes. Furthermore, the construction of these models is often monolithic: they do not allow one to readily modify the processes involved or include the new ones, or to combine models at different scales. We show how to construct a simple model of immune response to a respiratory virus and a model of transmission using an easily modifiable set of rules allowing further refining and merging the two models together. The immune response model reproduces the expected response curve of PCR testing for COVID-19 and implies a long-tailed distribution of infectiousness reflective of individual heterogeneity. This immune response model, when combined with a transmission model, reproduces the previously reported shift in the population distribution of viral loads along an epidemic trajectory. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.


Subject(s)
COVID-19 Testing , COVID-19 , Humans , Immunity
3.
BMJ Global Health ; 7:A35, 2022.
Article in English | EMBASE | ID: covidwho-1968281

ABSTRACT

Objective The health systems costs of COVID-19 are high in many countries, including Pakistan. Without increases in fiscal space, COVID-19 interventions are likely to displace other activities within the health system. We reflect on the inclusion of COVID-19 interventions in Pakistan's Essential Package of Health Services (EPHS) and, from a financial optimisation perspective, propose which interventions should be displaced to ensure the highest possible overall health utility within budgetary constraints. Methods We estimated the costs of all 88 interventions currently included in the EPHS and collected published data on their cost-effectiveness. We also estimated total costs and costeffectiveness of COVID-19 vaccination in Pakistan. We ranked all EPHS interventions and COVID-19 vaccination by costeffectiveness, determining which interventions are comparatively least cost-effective and, in the absence of additional funding, no longer affordable. Results The EPHS assumes a spending per capita of US $12.96, averting 40.36 million disability-adjusted life years (DALYs). From a financial optimisation perspective, and assuming no additional funds, the introduction of a COVID-19 vaccine (US$3 per dose) should displace 8 interventions out of the EPHS, making the EPHS more cost-effective by averting 40.62 million DALYs. A US$6 dose should displace a further intervention and avert 40.56 million DALYs. A US$10 dose would partially fall out of the package, displacing four additional interventions. If health spending per capita decreased to US$8, a US$3 dose would still be affordable, but not US$6 or US$10 doses. Discussion Cost-effectiveness is only one criterion considered when deciding which interventions are included in (or removed from) a health benefits package. While displacing certain interventions to create fiscal space for the COVID-19 vaccine may lead to a financially optimal scenario, doing so may be politically unfeasible or socially undesirable. We highlight the difficult trade-offs that health systems face in the era of COVID-19.

5.
MEDLINE; 2021.
Preprint in English | MEDLINE | ID: ppcovidwho-329762

ABSTRACT

Mobility data have demonstrated major changes in human movement patterns in response to COVID-19 and associated interventions in many countries. This can involve sub-national redistribution, short-term relocations as well as international migration. In this paper, we combine detailed location data from Facebook measuring the location of approximately 6 million daily active Facebook users in 5km 2 tiles in the UK with census-derived population estimates to measure population mobility and redistribution. We provide time-varying population estimates and assess spatial population changes with respect to population density and four key reference dates in 2020 (First lockdown, End of term, Beginning of term, Christmas). We also show how the timing and magnitude of observed population changes can impact the size of epidemics using a deterministic model of COVID-19 transmission. We estimate that between March 2020 and March 2021, the total population of the UK has declined and we identify important spatial variations in this population change, showing that low-density areas have experienced lower population decreases than urban areas. We estimate that, for the top 10% highest population tiles, the population has decreased by 6.6%. Further, we provide evidence that geographic redistributions of population within the UK coincide with dates of non-pharmaceutical interventions including lockdowns and movement restrictions, as well as seasonal patterns of migration around holiday dates. The methods used in this study reveal significant changes in population distribution at high spatial and temporal resolutions that have not previously been quantified by available demographic surveys in the UK. We found early indicators of potential longer-term changes in the population distribution of the UK although it is not clear how these changes may persist after the COVID-19 pandemic.

6.
PUBMED; 2021.
Preprint in English | PUBMED | ID: ppcovidwho-293295

ABSTRACT

Governments around the world have implemented non-pharmaceutical interventions (NPIs), e.g. physical distancing and travel restrictions, to limit the transmission of COVID-19. While lockdowns and physical distancing have proven effective for reducing COVID-19 transmission, there is still limited understanding of the degree to which these interventions impact disease transmission, and how they are reflected in measures of human behaviour. Further, there is a lack of understanding about how new sources of data can be used to monitor NPIs, where these data have the potential to augment existing disease surveillance and modelling efforts. In this study, we assess the relationship between indicators of human mobility, NPIs, and estimates of R t , a real-time measure of the intensity of COVID-19 transmission in subnational districts of Ghana using a multilevel generalised linear mixed model. We demonstrate a relationship between reductions in human mobility and decreases in R t during the early stages of the COVID-19 epidemic in Ghana, and show how reductions in human mobility relate to increasing stringency of NPIs. We demonstrate the utility of combining local disease surveillance data with large scale human mobility data to augment existing surveillance capacity to estimate and monitor the effect of NPI policies. Summary Box: What is already known?: NPI measures including physical distancing, reduction of travel, and use of personal protective equipment have been demonstrated to reduce COVID-19 transmission. Much of the existing research focuses on comparisons of NPI stringency with COVID-19 transmission among different countries, or on high-income countries. What are the new findings?: We show how human mobility and NPI stringency were associated with changes in R t using detailed COVID-19 surveillance and human mobility data from districts in Ghana. We further demonstrate how this association was strongest in the early COVID-19 outbreak in Ghana, decreasing after the relaxation of national restrictions. What do the new findings imply?: The change in association between human mobility, NPI stringency, and R t may reflect a "decoupling" of NPI stringency and human mobility from disease transmission in Ghana as the COVID-19 epidemic progressed. This has implications for public responses to the early stages of epidemic outbreaks and our understanding of the utility of mobility data for predicting the spread of COVID-19.

7.
PUBMED; 2021.
Preprint in English | PUBMED | ID: ppcovidwho-292934

ABSTRACT

Governments around the world have implemented non-pharmaceutical interventions (NPIs), e.g. physical distancing and travel restrictions, to limit the transmission of COVID-19. While lockdowns and physical distancing have proven effective for reducing COVID-19 transmission, there is still limited understanding of the degree to which these interventions impact disease transmission, and how they are reflected in measures of human behaviour. Further, there is a lack of understanding about how new sources of data can be used to monitor NPIs, where these data have the potential to augment existing disease surveillance and modelling efforts. In this study, we assess the relationship between indicators of human mobility, NPIs, and estimates of R t , a real-time measure of the intensity of COVID-19 transmission in subnational districts of Ghana using a multilevel generalised linear mixed model. We demonstrate a relationship between reductions in human mobility and decreases in R t during the early stages of the COVID-19 epidemic in Ghana, and show how reductions in human mobility relate to increasing stringency of NPIs. We demonstrate the utility of combining local disease surveillance data with large scale human mobility data to augment existing surveillance capacity to estimate and monitor the effect of NPI policies. Summary Box: What is already known?: NPI measures including physical distancing, reduction of travel, and use of personal protective equipment have been demonstrated to reduce COVID-19 transmission. Much of the existing research focuses on comparisons of NPI stringency with COVID-19 transmission among different countries, or on high-income countries. What are the new findings?: We show how human mobility and NPI stringency were associated with changes in R t using detailed COVID-19 surveillance and human mobility data from districts in Ghana. We further demonstrate how this association was strongest in the early COVID-19 outbreak in Ghana, decreasing after the relaxation of national restrictions. What do the new findings imply?: The change in association between human mobility, NPI stringency, and R t may reflect a "decoupling" of NPI stringency and human mobility from disease transmission in Ghana as the COVID-19 epidemic progressed. This has implications for public responses to the early stages of epidemic outbreaks and our understanding of the utility of mobility data for predicting the spread of COVID-19.

8.
PLoS ONE ; 16(2), 2021.
Article in English | CAB Abstracts | ID: covidwho-1410599

ABSTRACT

Background: The success of a government's COVID-19 control strategy relies on public trust and broad acceptance of response measures. We investigated public perceptions of the UK government's COVID-19 response, focusing on the relationship between trust and perceived transparency, during the first wave (April 2020) of the COVID-19 pandemic in the United Kingdom.

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